LLM Mart Basic

Predict protein 3D structures with AlphaFold2 via ColabFold — MMseqs2-accelerated MSAs, monomer and AlphaFold2-Multimer complex folding, and confidence-based validation (pLDDT, pTM/ipTM, PAE). Use when folding a protein sequence or complex from FASTA, generating a predicted struc

Build, slice, concatenate, read, and write AnnData annotated data matrices (obs, var, X, layers, obsm, uns) — the scverse data STRUCTURE, not an analysis pipeline. Use when creating or wrangling .h5ad/zarr files, managing cell and gene annotations, concatenating batches, or handl

Infer gene regulatory networks (GRNs) from expression matrices using arboreto's scalable GRNBoost2 and GENIE3 tree-ensemble algorithms with Dask-distributed computation. Use when analyzing bulk or single-cell RNA-seq transcriptomics to map transcription-factor-to-target-gene regu

Manipulate biological sequences, parse FASTA/GenBank/PDB files, run phylogenetics, and access NCBI/PubMed programmatically via Biopython (Bio.SeqIO, Bio.Entrez, Bio.PDB, Bio.Blast). Use when scripting custom bioinformatics pipelines, batch-processing sequence files, automating BL

Query 40+ bioinformatics web services through one consistent Python API with bioservices (UniProt, KEGG, ChEMBL, Reactome, Ensembl, NCBI and more). Use when a workflow must hit multiple databases together, map identifiers across services, or run cross-database analyses — for quic

Runs NCBI BLAST+ 2.17.0 sequence searches from the command line: makeblastdb (with -parse_seqids), blastn/blastp/blastx/tblastn with tabular -outfmt 6/7 for parsing, correct -task choice (megablast vs blastn vs blastn-short), -taxids/-negative_taxids taxonomic scoping, and -mt_mo

Co-fold biomolecular complexes with Boltz-2, an open AlphaFold3-style model — predict protein + ligand (SMILES/CCD), protein + nucleic-acid, and multi-chain structures in one pass, with binding-affinity prediction. Use when folding a protein together with a small-molecule ligand,

Predict genome-wide functional genomics tracks from DNA sequence with Borzoi (Linder 2025) — a sequence-to-function model outputting RNA-seq, CAGE, ATAC, and ChIP coverage across long context, used to score non-coding and regulatory variant effects. Use when predicting functional

Query the CZ CELLxGENE Census (200M+ cells) programmatically via cellxgene-census and TileDB-SOMA, slicing expression by tissue, disease, or cell type and returning AnnData. Use when pulling reference single-cell RNA-seq data from the largest curated public atlas, running populat

Predict biomolecular complexes with Chai-1, an open AlphaFold3-style model that folds multi-entity assemblies (proteins, ligands, nucleic acids) from a single typed FASTA — strong on antibody–antigen and protein–ligand complexes, with optional MSA and restraint inputs. Use when p

Build and analyze genome-scale constraint-based metabolic models with COBRApy — flux balance analysis (FBA), flux variability analysis (FVA), gene and reaction knockouts, flux sampling, and SBML model I/O. Use when simulating metabolic networks, predicting growth or knockout phen

Process and visualize deep-sequencing coverage with the deepTools CLI — convert BAM to bigWig (bamCoverage), build log2 ratio tracks (bamCompare), run QC (multiBamSummary correlation, PCA, plotFingerprint), apply the ATAC-seq Tn5 shift (alignmentSieve --ATACshift), and make TSS/p

Run ESM protein language models — ESMC for embeddings and representations, ESMFold2 for structure prediction, and ESM3 for generative multimodal protein design across sequence, structure, and function — locally or through the hosted Biohub Platform API (formerly Forge). Use when

Manipulate, annotate, and render phylogenetic trees programmatically with the ETE Toolkit (ete3) — parse and edit Newick/NHX, detect duplication/speciation events, infer orthology and paralogy, query NCBI taxonomy, and export PDF/SVG figures. Use when traversing or reformatting t

Parse and write FCS (Flow Cytometry Standard) files v2.0-3.1 with FlowIO — extract event data as NumPy arrays, read $-keyword metadata and channel/parameter definitions, and convert events to CSV or pandas DataFrame. Use when loading raw .fcs flow-cytometry files, inspecting chan

Run fast one-liner queries to 20+ bioinformatics databases from the gget CLI or Python — gene info (Ensembl), BLAST, AlphaFold structures, Enrichr enrichment, and more. Use for quick interactive lookups of genes, sequences, structures, or pathways — for batch processing or advanc

Analyze and engineer protein glycosylation — scan sequences for N-glycosylation sequons (N-X-S/T), predict O-glycosylation hotspots, and reach curated glycoengineering tools (NetOGlyc, GlycoShield, GlycoWorkbench). Use when identifying or designing glycosylation sites, optimizing

Extract and preprocess tiles from whole-slide images (WSI) with histolab — OpenSlide-backed slide loading, tissue detection and masks, Random/Grid/Score tile extraction, and image/morphological filters for H&E preprocessing. Use when the user needs lightweight WSI slide preproces

Manage, annotate, and trace biological data with LaminDB, an open-source FAIR data framework that makes datasets queryable, versioned, and reproducible. Use when registering or querying biological datasets (scRNA-seq, spatial, flow cytometry), validating and curating data against

Design protein sequences around bound ligands, metals, and nucleic acids with LigandMPNN (Dauparas 2023) — inverse folding that conditions on non-protein context, so binding-pocket and metal-site residues are chosen to fit the actual ligand. Use when designing a small-molecule or

Every VM came back. The cluster did not. Declarative systems converge on config, and the datapath isn't config.

A surprising share of AI-in-the-terminal failures aren't the AI. They're zsh, and a version of bash from 2006.

A Claude Code plugin turns standalone project configuration into a namespaced, installable extension that teams and communities can update as one unit.

None of the safety came from the model. It came from six boring habits.

Skills package instructions and references. Subagents run work in a separate context and return results. They solve different problems and can be composed deliberately.

Six hours in, one step left, everything green, and the incident that didn't happen

CLAUDE.md carries persistent project context. Skills load reusable procedures when relevant. Separating stable facts from task-specific workflows keeps both easier to maintain.

Twenty minutes recovering secrets that never existed, and the one sentence from a human that ended it

An API request routing a model's tool call through an approval gate to a remote MCP server

31 config keys, two audits, and why the first one was wrong in both directions

The official MCP Registry stores standardized server metadata rather than package code. Publishers verify a namespace, describe installation or remote access, and submit immutable versions.

Everyone looks at the Dockerfile. The file that actually leaked the key was the project file.

Remote MCP authorization uses established OAuth standards, but secure integration still requires issuer validation, least-privilege scopes, protected token handling, and server-side enforcement.

"Copy it over and switch the reference" is two steps, and the outage lives in the one nobody checks

stdio fits local processes and prototypes. Streamable HTTP fits hosted services and shared integrations. The right choice follows where the capability runs and who must reach it.

The most important rule wasn't about what I could change. It was about what I was allowed to display.

Tools perform operations, resources expose readable context, and prompts provide reusable templates. Choosing the correct primitive makes an MCP server easier to understand and govern.

Use MCP Inspector to connect to local or remote servers, inspect capabilities, call tools, read resources, test prompts, and diagnose failures before release.

Build an MCP server in TypeScript with focused tools, validated schemas, local and remote transports, Inspector tests, and production security controls.

An MCP server exposes tools, resources, or prompts through a standard protocol so an AI application can discover and use external capabilities.

Command dispatcher for review.

Command dispatcher for tool.

浏览器操控。通过 CDP 协议控制 Chrome，复用已有登录态，执行浏览器自动化操作。

网文封面生成。分析书名题材，生成专业封面图。

网文去AI味。检测并清除文本中的AI写作痕迹，让文字回归自然。

逆向导入已有小说。将已写好的小说反向解析为标准项目目录结构。

长篇网文拆文。深度拆解爆款长篇小说的黄金三章、人设、爽点、节奏。

长篇网文扫榜。分析起点、番茄、晋江等平台排行数据，提炼市场趋势。

长篇网文写作。从大纲到正文，辅助长篇网络小说的创作。

多视角对抗式审查。使用多个 Agent 对作品进行多维度审稿。

网文写作环境部署与检查。部署 hooks、rules、agents、项目指令等基础设施；传入 check 只检查不改动。

短篇网文拆文。拆解爆款短篇的故事核、结构、情感线和反转设计。

短篇网文扫榜。分析知乎盐言、番茄短篇等平台热门数据。

短篇网文写作。辅助短篇小说创作，从构思到成稿。

网文工具箱路由入口。根据模糊意图自动分发到对应的写作、拆文或扫榜工具。

浏览器操控。通过 CDP 复用 Chrome 登录态执行浏览器自动化。

小说封面生成。根据书名、作者名和题材生成专业网文封面。

网文去 AI 味。检测并清理模板化、解释腔和过度工整表达。

逆向导入已有小说，将成稿或半成品解析为可续写项目。

长篇网文拆文，分析黄金三章、人设、爽点和长线节奏。

Implementation of Podlite markup language

Open-source AI video workbench. Bring any model or your local ComfyUI, and let Claude Code / Codex / Cursor direct it over MCP — storyboard, references, generat…

《深入理解 AI Agent：设计原理与工程实践》（李博杰 著）开源主仓库：全书正文、编译版 PDF 与按章配套代码

Distilly — Distill how they think into reusable Skills for any Agent or Bot. Formerly Colleague Skill（原同事 Skill）.

本地优先的类飞书 Markdown 编辑器,内置可审改的 AI 助手 | Local-first WYSIWYG Markdown editor with a reviewable AI agent

A lightweight all-in-one terminal with 20+ protocols — SSH, RDP, SFTP, databases, Kubernetes and more. With a built-in autonomous AI Agent that plans and runs m…

一款专注于桌宠方向的AIAgent。特点是一键安装、功能齐全、极低开销、完全暴露上下文、全功能插件化、AI自主插件开发、永久唯一会话、类游戏引擎交互策略。具有极高的扩展性和拟人程度上限，非常适合想长期培养和自定义需求高的用户。

Control Gmail, Google Calendar, Docs, Sheets, Slides, Chat, Forms, Tasks, Search & Drive with AI - Comprehensive Google Workspace MCP Server & CLI Tool

一个先接住情绪、再分析关系并给出可执行策略的 Codex 恋爱军师，内置心理、法律、社会、人文、哲学、婚姻家庭与性学知识库，支持多元关系。

AI-powered SRE platform — read-only infrastructure diagnostics with deep investigation, security governance, and team collaboration

An open-source AI desktop companion inspired by Cyrene, combining immersive Chat, personalized long-term memory, and an agentic Work mode.

A local-first AI agent with persistent memory, emotional intelligence, and a peer-to-peer skills economy.

The open-source, multi-agent alternative to Claude Tag. @ any agent, wherever work happens, your agents work alongside your team and each other, learning as the…

Simple LLM service identification - translate IP:Port to Ollama, vLLM, LiteLLM, or 60+ other AI services in seconds

🔥 Official Firecrawl MCP Server - Adds powerful web scraping and search to Cursor, Claude and any other LLM clients.

Claude in Chrome, reverse-engineered and open-source. No domain blocklist. Any Chromium browser. Same 18 MCP tools, same performance.

Agent-native flight & hotel search and booking — MCP server, CLI, and Python/JS SDKs. Hundreds of airlines plus the major booking sites, with per-flight reliabi…

Open-source desktop AI agent for tools, files, knowledge, workflows, and real deliverables.

Open-source AI job search: scan job portals, evaluate listings into a structured A-H report with a global 1-5 score, tailor your CV, track applications — runs l…

Privacy-first Codex skill for discovering, validating, completing, and tracking job applications